From: jprocter <Jim Procter>
Date: Tue, 14 Jun 2005 15:44:03 +0000 (+0000)
Subject: Arbitrary decision to keep friendly id name when reading in uniprot headered fastA... 
X-Git-Tag: Release_2_0~39
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ea7f74cc42770ce2f0dbb6745cb221eabf98e181;p=jalview.git

Arbitrary decision to keep friendly id name when reading in uniprot headered fastA files.
---

diff --git a/src/jalview/io/FastaFile.java b/src/jalview/io/FastaFile.java
index 7e7e06b..adfa967 100755
--- a/src/jalview/io/FastaFile.java
+++ b/src/jalview/io/FastaFile.java
@@ -53,6 +53,9 @@ public class FastaFile extends AlignFile {
         while ((line = nextLine()) != null) {
             if (line.length() > 0) {
                 // Do we have an id line?
+                // JBPNote - this code needs to be standardised to EBI/whatever for the
+                // >dbref/dbref/dbref|refid1|refid2|refid3 'human-readable' style of naming (should it really exist)
+
                 if (line.substring(0, 1).equals(">")) {
                     if (count != 0) {
                         if (sstart != 0) {
@@ -73,17 +76,18 @@ public class FastaFile extends AlignFile {
                     id = id.substring(1);
 
                     com.stevesoft.pat.Regex dbId = new com.stevesoft.pat.Regex(
-                            "[A-Za-z-]+/[A-Za-z-]+\\|(\\w+)\\|(.+)");
-
+                            "[A-Za-z-]+/?[A-Za-z-]+\\|(\\w+)\\|(.+)");
+                    // JBPNote At the moment - we don't get rid of the friendly names but this
+                    // behaviour is probably wrong in the long run.
                     if (dbId.search(id)) {
                         String dbid = dbId.stringMatched(1);
                         String idname = dbId.stringMatched(2);
-
-                        if ((idname.length() > 0) &&
-                                (idname.indexOf("_") > -1)) {
-                            id = idname; // just use friendly name // JBPNote: we may lose uniprot standardised ID here.
-                        } else {
-                            id = dbid; // use dbid to ensure sensible queries
+                        if ( (idname.length() > 0) &&
+                             (idname.indexOf("_") > -1)) {
+                          id = idname; // use the friendly name - apparently no dbid
+                        } else
+                        if (dbid.length()>1) {
+                            id = dbid; // ignore the friendly name - we lose uniprot accession ID otherwise
                         }
                     }